Secret Weapon
by Raphs No.1 Girl
Summary: Sequel to Turtle Against the World - plz read that first! :D Raphael has been gone for two years, when he is captured by a mysterious organisation, and used as their secret weapon! But who will he be used against?
1. Chapter 1

**_Hey all, this is the sequel to Turtle Against the World, so please read that first if you haven't already done so. :D_**

**_This is thanks to raphfreak, for suggesting I do a sequel and for beta-reading this chapter for me. You rock, dudette! ;)_**

**_DISCLAIMER: Still don't own them - but they're top of my list for Santa! ;D_**

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It had now been near on two years since Raph had left home, and yet the rest of the family still felt his absence as strongly as if it had only been yesterday.

When setting the table for dinner, somehow someone always set a fifth place for the absent turtle, and they still bought Christmas and birthday presents for him, which were now sitting in a corner of his bedroom, awaiting his return. They were still expecting their brother to come back to them – not one of them allowed themselves to consider that he may be gone forever. They had caught glimpses of him several times; always sensed him watching them when they were out on patrol, and even found Christmas and birthday presents left for them just outside the Lair.

Yet, despite their exhaustive efforts, they had never managed to find out where he was living now, or been able to talk to him. At first, Donny had hoped they could track Raph down using the signal from his shell-cell, but they had soon discovered it abandoned in a sewer tunnel; clearly Raphael didn't want to be found. It was now almost Christmas again, and they were all beginning to hope that perhaps this would be the year Raph would come home.

Mikey was absent-mindedly flipping through the TV channels while he waited for Donny to return with his repaired games console, which had had an unfortunate accident involving a couple of shuriken, thrown by an annoyed Mikey after he failed to pass the next level of his game for the twelfth time in a row. He was about to switch the TV off when he landed on a news channel. Usually, he didn't watch the news, but something about the story caught his eye. There on the screen was an image of a Purple Dragon tattoo. Mikey quickly turned up the volume, to hear the female news reporter saying,

"…in an alleyway by an abandoned apartment block. It seems there was some sort of gang altercation – numerous bodies were found. Most had been stabbed using some sort of three-pointed weapon, which forensics experts are currently trying to identify.

"Raph!" Mikey breathed, before yelling, "Hey guys! Come look at this on the news!" Leo, Donny, and Master Splinter rushed to the living room – it had to be something really interesting to make Mikey watch the news! The reporter continued,

"…however, the most surprising victim was a large male, who has been identified by an anonymous source to be the leader of the infamous Purple Dragon street-gang: a man known as "Hun". His mutilated body, wounds seemingly inflicted by the same three-pointed blade, was found several yards from the site where the other victims' bodies were found."

"Hun is dead?!" Leo was shocked.

"Three-pointed weapon?" Donny was considering. "Guys, you don't think – could it be Raph's sai?"

"C'mon, dudes, its gotta be Raph!" Mikey whooped. "And he's taken down Hun and dozens of Purple Dragons!"

"My sons, please be quiet! I am trying to listen!" Master Splinter's face was creased in concentration as he tried to hear what the news reader was saying. The three turtles quickly fell silent, Mikey still bearing a huge grin on his face.

"…FBI did find a blood-trail leading from the crime scene, but were unable to track down the perpetrator. The NYPD are asking anyone with any information to contact them as a matter of urgency. In other news, NASA launched the shuttle…"

"A blood-trail? Guys, if it really was Raph, it sounds like he's hurt – maybe we should go look for him?" Donny asked, wishing the woman had said how much blood there had been.

"But surely if he's hurt, he'll come home anyway?" Mikey said.

"Maybe Mikey, but this happened last night, right?" Leo asked, and Mikey nodded in response. "So, if Raph was coming back, surely he'd be here by now? Maybe Don's right –"

"My sons, perhaps it would be a good idea to search for Raphael. I will wait here, in case he should return while you are out."

"Hai sensei." The three turtles bowed respectfully. Just as they were about to leave, Leo's shell-cell started ringing.

"Hello? April?"

"Leo, did you see the news?"

"Yes, April. We're just heading out now to investigate, and look for Raph."

"That's what I'm calling about. We had a break-in last night –"

"April, can we talk about this later? How about we drop in when we're done searching?"

"No, Leo, you don't understand! I think you're really going to want to hear this."

Leo sighed. "Alright, April. What is it?"

"Like I said, someone broke in last night. They got in through the bathroom window, which we'd accidentally left open. The odd thing was, they only stole medical supplies, like bandages and antiseptic creams. There was also some blood on the floor. I've only just put two-and-two together after seeing that news report!"

"So, you're saying Raph came to your place to get medical supplies?"

"I think so. There was a bit of blood around, but we cleaned it up earlier, before we found out about the gang fight. I'm sorry, Leo."

"Don't worry, April – if Raph was there, we should be able to find something. We'll be there in a couple of minutes, okay?"

"Of course it's okay, Leo. See you soon." They disconnected the call, and Leo put the shell-cell back in his belt with a heavy sigh.

"What's up, dude?" Mikey asked, knowing immediately from his older brother's facial expression that he had just found out something crucial about their missing sibling.

"That was April. She said Raph took some medical supplies from her place."

"Did she see him? Is he still there?"

"No, and no, Mikey. He just took the stuff and left."

"But surely there'll be a blood-trail we can follow, or something?"

Leo shook his head, "Casey and April cleared it up. They've only just realized it could have been Raph, after seeing that report on the news."

"How are we gonna find him now, Leo?"

"I don't know, Mike. But we sure as shell will find him and bring him home."

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_**Please review and let me know if I should continue with this! Thanks. :D**_


	2. Chapter 2

**_Hiya. Yes, I know this is a couple of days late, but I've been having so much trouble with Deal With The Devil, and there was the Easter weekend, etc, etc- basically I've been super busy. So, anyways, sorry its late._**

**_Thanks to raphfreak for being my beta-reader! :)_**

**_DISCLAIMER: I don't own TMNT, but I do own the OCs (in this chapter, they would be Joey and Bert). ;)_**

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After an extensive search at April's apartment and around the scene of the gang fight, the remaining three turtles dejectedly headed home empty-handed.

"We'll look again tomorrow night," Leo assured his younger siblings. "Remember what Raph said that time Master Splinter went missing after a battle with The Shredder? I asked him how he was going to search an entire city, and he said "one block at a time". I think that's what we're going to have to do."

"We'll have to do this systematically," put in Donny. "Maybe if we split the city into sectors, and work out who's going to search where?"

"Good idea, don. We'll sort that out in the morning. For now, I think we all need to get some rest."

"But Leo – I'm not even tired," Mikey protested, trying to stifle a yawn.

Leo managed a half-smile at his baby brother, and said firmly, "Bed." he sighed as he watched his orange- and purple-masked brothers amble off to their rooms, sincerely doubting that either of them would get a restful sleep, if they managed to sleep at all. He could see the flickering light from candles being emitted from his sensei's chamber, showing that he was still awake. Leo was tempted to enter and talk with him, but decided against it and instead went to his own bedroom, where he attempted to get some sleep.

*******

It was icy cold, with a northerly wind blowing across the city, bringing with it sheets of rain. In his shelter, covered in a thin blanket, Raph could feel the freezing chill in the air.

"Geez, it really sucks to be cold-blooded – especially in the middle of an NYC winter!" Raph muttered to himself. He noticed he'd been doing that a lot lately, talking to himself. "I've been on my own too long."

He would never admit, not even too himself, just how much he missed his brothers, his family, his friends. He especially felt it now that Christmas was drawing closer. He hoped they knew he was thinking about them – he left Christmas and birthday presents just outside the Lair, to let them know he still cared, and last time he checked they weren't there. He had secretly hoped they might leave something for him, but they didn't. This either meant that they hadn't found the gifts, or that they didn't care about him anymore. He hoped it wasn't the latter, but it was this fear that had kept him from returning home.

He had thought about going back after he'd taken down Hun the night before, but didn't think he could bear it if his brothers rejected him when they saw him. After all, he'd been gone two years, only seeing them briefly when he aided them in battle, but never letting them get close enough to touch him or speak to him. He shifted his weight, drawing in a sharp intake of breath as the stitches on his leg pulled. He tossed the blanket partially aside to check the row of roughly-done stitches which had been sewn along the length of a long gash on his thigh. He could tell by looking at it that it was becoming infected, and his rough handiwork would leave a scar there. Reaching into a bag, he pulled out a tube of antiseptic cream, and smoothed it over the wound, not even flinching as it began to sting.

He felt bad for having to steal from Casey and April, but knew he couldn't have risked them seeing him, just in case they rejected him as well. He resolved that as soon as he found some more money, he would leave it in their bathroom, to pay them back. But for now, survival was priority number one. Wrapping the blanket back around himself, he knew he had to stay awake. However, he found his eyelids growing too heavy to keep open, and within a few minutes he was in a deep sleep. As he slept, his reptilian body became torpid: his heart rate slowed, his lungs almost ceased to breathe, and his body temperature fell. And as his body entered this state of torpor, the temperature in New York plummeted and snow began to fall.

************

In the Lair, everyone was suddenly jerked awake by the harsh beeping of an alarm. Donny shot up and ran to his work station. With a few taps on his computer keyboard, the alarm fell silent. He turned around to find Leo, Mikey and Master Splinter standing behind him.

"Donatello, my son what was that alarm?" The elderly rat's ears were pricked up, listening intently for any sounds of approaching danger.

"It was from my weather monitor. The temperature outside has fallen below freezing, and we've probably had some snow." Donny explained.

"But Raph's out there!" Mikey wailed.

"Don't worry, Mikey, I'm sure Raph'll be fine. Right, Don?" Leo looked pleadingly at the purple-masked turtle, begging for his reassurance.

"Well, er…" Donny rubbed his hand on the back of his neck.

"Donny, what are you not telling us?" Leo's arms were now crossed as he stared at him.

"Um…well, with us being cold-blooded, cold weather is obviously a bad thing for us," he glanced at Master Splinter, who nodded to tell him to continue. "When we get too cold, our bodies go into a kind of, erm…hibernation, known as 'torpor'. But if the temperature goes too low while we're in a torpid state, our bodies could freeze, which obviously causes death." As he finished, he stared at his feet, avoiding eye contact with them. They were all silent for a moment. Then,

"So, dudes, shouldn't we, like, go out and look for Raph?" Mikey broke the silence.

Leo sighed, "But Mikey, we don't know where he is, remember? We looked last night, but found no trace of him."

"Hang on, Leo, Mikey's right. But how to find him?" Donny tapped his chin in thought with one of his green fingers, before suddenly clicking his fingers in an 'I've-got-it' gesture. "Of course! Master Splinter, as a rat, you have a highly developed sense of smell, right?"

"Of course, my son," his sensei nodded.

"And you can both sense and smell us, right?"

"Ah, my son – I think I see what you are suggesting now!"

"Well I sure don't!" Mikey snapped in annoyance.

"What they're saying is, if we take Master Splinter with us, he might be able to find Raph by smelling or sensing him," Leo explained.

"Ooohhh," Mikey nodded, now understanding.

"Do you think you can do it, Master?" Donny was still questioning the rat.

"I can but try, Donatello. But you must all dress warmly before we leave – I do not want any of you falling ill!" But his remaining three sons had already dashed off to their rooms to get ready.

************

"Awww, c'mon Joey, its freezing!"

"Shuddup, Bert! Da boss says we gotta get it, so we gotta get it, got it?!"

"Erm…yeah…no…not really."

The man called Joey growled in annoyance, "Just keep an eye out for it, okay? Da boss'll have our heads on a plate if we don't deliver this time."

"Okay, Joey. But how are we gonna find it?"

"Bert, are you naturally this stupid, or do ya have to work at it? I already told ya, we track it using this device. Hun managed to get the tracker on it, before the thing took him down."

"How do we know its not gonna attack us?"

"It's too cold – things like that go to sleep when it gets too cold. Now shuddit, according to this tracker thing, it's somewhere round here, down that alleyway."

The two men fell silent as they searched the area. Despite his confidence that their quarry would be in no fit state to fight them, Joey was a little nervous – after all, this thing had managed to take out Hun, something which everyone had thought was near on impossible to do. He swallowed hard, glancing again at the tracker screen: the marker hadn't moved, which either meant it was asleep, or it was lying in wait for them.

"Psst, Bert!" Joey hissed, "We're close to it. Have you found anything yet?"

"Not yet, Joey," Bert whispered in response, "I can't see…huh? What's that? Joey, I think I found it!"

Joey shone his torch into the makeshift shelter. He grinned maliciously, "Bingo." The he turned to Bert, "Call it in, Bertie-boy! Tell 'em we found it!"

"You got it, Joey!" he replied, pressing a button on his cell phone.

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**_I hope that was okay - I'll do my very best to make sure the next chapter is on-time._**

**_Also, while I'm here, have you checked out fics by raphfreak and Simone Robinson? If not, then why not?! Simone is also running a contest on Deviant Art (see Simone's profile for a link). :)_**


	3. Chapter 3

**_Yes, this chapter has been a very very long time in coming, and I'm sorry. But its here now, and thats the main thing - isn't it? :S_**

**_Anyway, sorry it isn't very long - writen down it was like 5 A4 pages (okay, so I have quite big handwriting, but still), but when I typed it up it wasn't very long at all. Oh well, hope you like it all the same. And don'twrite thsi off as one if the usual Raph-torture fics - in a few chapters I think you'll all be getting a major shock! ;D_**

**_DISCLAIMER: Still don't own them. :( [All I own is the OCs.] _**

"Here, my sons, down this alleyway."

They had been searching for hours and so far their efforts had been fruitless. It seemed as though Raphael had disappeared off the face of the Earth.

This wasn't the first alley they had stopped and searched, but something in Master Splinter's voice told them that this was definitely the place. They all exited the Battle-Shell, but allowed their sensei to look around on his own. He was about halfway down the alley when he gave a sudden gasp. Alarmed, the three turtles ran to his side.

"What is it, sensei?" Leo asked, looking at the old rat's face with concern. He pointed a shaking furry finger at the ground. In the shallow sprinkling of snow, strange marks had been made, the snow turned slightly pink with a spattering of blood and – now they all gasped. There, sitting in the midst of the discoloured snow, was a sai. It was instantly recognisably from the red wrapping on the handle, the same cloth his mask had been made from – it was Raph's!

Crouching down, Donny examined the markings in the snow,

"Guys, these look like drag marks."

"What are you saying, Don?"

"Dude, you think Raph's been turtle-napped?!" Mikey almost burst out laughing at the thought of some poor person trying to catch his older brother. He noticed Leo's mouth twitch with a small smile at the thought too.

"It's possible, yes."

"But Donny, he took down Hun! And you and me both know it would be pretty much impossible for anyone to catch Raph, even if he's wounded."

"Not if he's gone into torpor already." Donny said seriously. Mikey fell silent – he'd forgotten about that possibility. He then glanced at his father and brothers,

"So, whadda we do now?"

They all looked at the floor, no one quite knowing what to say.

"I don't know, Mikey." Leo broke the silence, still not lifting his gaze from the ground.

* * *

"Urgh," Raph groaned as consciousness began to return to him. He was surprised to feel strong heat around him, instead of the icy winter wind he had been expecting. Wondering where he was, he cracked his eyes open a fraction, but quickly squeezed them shut to block out the bright light. But an overwhelming need to know where he was forced him to open his eyes again. After his eyes became used to the light, he opened them fully and looked around him.

He was surprised to find himself lying on a sandy floor, with a shallow pool of water in the corner. Looking above him, a series of red ceiling lamps were radiating the heat he felt, and several white light bulbs were emitting the bright white light that had hurt his eyes when he first woke up. With a severe sinking feeling and a shudder, Raph realised that he had seen something like this before.

_It was a few years ago now, maybe when they were about thirteen. He was topside with Mikey, and on their way to the skate-park they had passed a pet shop. Unsurprisingly, Mikey had insisted on having a look, and pushed his face up against the glass. Raph was also curious, but didn't want to admit it so, acting as if he wasn't interested, he had looked into the shop window as well. There, the two brothers had seen something that had fascinated them both: just inside the window, in a glass tank, was a little turtle. They had been so excited, they'd completely forgotten about going to the skate park and instead rushed home to tell the others about the little turtle they'd seen. Donny had later told them that the glass tank the turtle was in was called a terrarium, and it was what humans used to keep reptilian pets in._

As Raph continued his search around the area, he soon discovered that all four wall were made of glass, but three had been covered with some sort of background paper, which had an image of blue sky depicted on it. With horror he now knew where he was, or rather _what he was in_ – it was a terrarium!

As if to add insult to injury, they had also stripped him of his weapons, belt and mask, so that his reflection looked embarrassingly naked. In anger, Raph picked up one of the large, heavy rocks that surrounded the pond, and hurled it at the glass. However, instead of smashing through the glass as expected, the rock simply bounced off it, not leaving so much as a scratch on its surface. Now even angrier, he tried again – only to achieve the same results.

He tried repeatedly, but still did not to seem to be able to do the least bit of damage to the transparent wall. He was just about to throw the rock again when,

"Yo! Would ya stop doin' that?! That stuff's expensive, ya know?"

Whirling around, Raph instinctively tried to reach for his sais, which obviously weren't there. He bared his teeth at his captor and snarled,

"What?! Ya think ya can just take me prisoner, an' I'm gonna treat the cage nice?! That's not how it works, pal! So, unless ya want yer pricey tank demolished, I suggest ya let me go – NOW!"

"I don't think so, Raphael." With a growl, Raph stared at the woman who stepped out of the shadows. She was of small build, with a pretty face which could have looked very innocent if it wasn't for the sense of confident power Raph felt exuding from her.

She stepped up to the tank, her eyes on a level with Raphael's. For that one moment, as Raph looked into her dark-brown eyes rimmed with long, black lashes, he felt as if he could become lost in those eyes. For the briefest second, her eyes softened, but quickly narrowed back into a wicked expression. She continued to stare directly into his eyes, daring him to challenge her.

Something about this young woman unnerved him, and he quickly stepped back. A triumphant glint flashed across her face, but she remained where she was.

"How d'ya know my name?" he growled at her.

She gave a small, mirthless laugh and replied in a strong British accent,

"I make it my business to know everything about my prey."

"Ya mean you're –" he glanced between the muscular male and the petite female, eyes narrowed in confusion. His eyes landed once again on the young woman. With a dark smile, she finished in a victorious tone,

"Yes, Raphael – you are MY prisoner!"

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**_Okay, you all know the drill - I really like reviews, and they encourage me to update. *Hint, hint* ;)_**

**_I reply to all my reviews with a personal message, to show my appreciation. Obviusly I can't reply to anonymous reviews, so its best if you log in (although this is up to you, of course!). _**

**_I promise I will update as soon as I can. :)_**

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	4. Chapter 4

**_Sorry this is such a short chapter - all the same, I hope you like it! :)_**

**_DISCLAIMER: I don't own them, I only own the OCs. :(_**

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"But…but –you're a girl!" Raph snorted indignantly.

"Now, now, Raphael – I never took you to be the chauvinistic type. Actually, I had you down as more of a bad-boy-ladies-man." She chuckled before continuing, "I bet you'd've had all the girls trailing around after you – if you were human, that is."

At this moment, Raph was more grateful than he had ever been in his life, for he was sure that otherwise his face would be as red as his mask. Embarrassment was an odd emotion for the usually hot-headed turtle – there was something about this mysterious girl, something that unnerved him and made him feel all these emotions which had lain dormant for so long, but he couldn't quite put his finger on just what it was. Trying desperately to hide his raging emotions, he responded gruffly,

"Look, lady, I ain't got the time to sit around here chit-chatting with ya. I gotta go –"

"Go where? Do what? If my guys hadn't found you when they did, you'd be dead right now!"

"My bros woulda found me and –"

"And what? Taken you home? And everything would be like you'd never left? Don't kid yourself, Raph – you had the opportunity to go home after you killed Hun, but did you?" she now had her arms folded across her chest, and was glaring at him with a steely expression. Raph did not look up to make eye contact, and she saw his shoulders sag slightly.

"Oh Raph…" she sighed, uncrossing her arms and letting them fall to her sides.

"NO WAY!" she was slightly startled by the sudden loud roar from the terrarium, and looked up to see a very angry and upset mutant staring back at her. "Don't ya dare start feelin' sorry fer me! I don't need yer pity – I don't need nuthin' from ya!"

"Fine then," she spoke softly, her voice laced with an icy-calm tone. Continuing to stare unflinchingly into the turtle's wild-eyed glare, she snapped her fingers. The muscular man was beside her in an instant. She whispered something in his ear and he nodded in response, before quickly leaving the room.

Still looking at her captive, she produced a remote control from her pocket. She pressed a button and the glass became an opaque black, leaving Raph staring at his own reflection. With a roar, he punched the wall – he knew it would have no effect, but doing it made him feel better. He kept on hitting it for several minutes, until finally slumping down onto the sandy floor to ponder upon the situation he now found himself in.

****************

"Right, gentleman – listen up!" Her voice was only raised ever so slightly, yet the room immediately fell silent, and all eyes were turned towards her. Unperturbed by all this attention, she went on,

"We have the turtle, Raphael, in our possession, but he does not yet truly belong to us. He has a strong spirit – he's a fighter, and will not simply choose to comply with orders. We will first have to break him –"

"Alright! Where first – arms? Legs?" A large man with bulging muscles, somewhat resembling Hun, had stood up at the back of the room. He cracked his knuckles, and started punching his fist into his palm in anticipation of the beating.

"Down, Rambo!" she spoke sternly, and with a click of her fingers, like an obedient dog, the man returned to his seat. With a nod of approval, she continued, "Simply breaking his body will not affect his spirit. For that, we must use a method often used to break wild animals: starvation. He shall be left alone, without so much as a drop of water or crumb of food for at least three days. Only I shall see him daily. Am I understood?"

"Yes, mistress!" was the response from all within the room.

"Good." She smiled for a moment, before pointing at three of the men, "Rambo, Joey, and Bert, you shall come with me. And bring the chains. Everyone else – dismissed!" She then strode confidently out of the room, closely followed by Rambo, Joey and Bert.

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**_I will update as soon as I can!_**

**_Please review - I respond personally to each one (as long as you are logged in/verified). :)_**


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